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- PDB-5xqj: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Pe... -

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Basic information

Entry
Database: PDB / ID: 5xqj
TitleCrystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose
ComponentsPcrglx protein
KeywordsLYASE / exo-rhamnogalacturonan lyase / enzyme / pectin / SAD / Se
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
YetA-like protein / : / : / : / PcRGLX-like N-terminal RIFT barrel domain / PcRGLX-like protein central beta sandwich domain / PcRGLX-like protein C-terminal alpha/alpha toroid domain
Similarity search - Domain/homology
Exo-rhamnogalacturonan lyase / Pc16g08050 protein
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKunishige, Y. / Iwai, M. / Tada, T. / Nishimura, S. / Sakamoto, T.
CitationJournal: FEBS Lett. / Year: 2018
Title: Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
Authors: Kunishige, Y. / Iwai, M. / Nakazawa, M. / Ueda, M. / Tada, T. / Nishimura, S. / Sakamoto, T.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pcrglx protein
B: Pcrglx protein
C: Pcrglx protein
D: Pcrglx protein
E: Pcrglx protein
F: Pcrglx protein
G: Pcrglx protein
H: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)809,03624
Polymers805,4548
Non-polymers3,58116
Water13,439746
1
A: Pcrglx protein
D: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,2186
Polymers201,3642
Non-polymers8554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-11 kcal/mol
Surface area58290 Å2
MethodPISA
2
B: Pcrglx protein
C: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,2186
Polymers201,3642
Non-polymers8554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-12 kcal/mol
Surface area58050 Å2
MethodPISA
3
E: Pcrglx protein
H: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,2186
Polymers201,3642
Non-polymers8554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-9 kcal/mol
Surface area58610 Å2
MethodPISA
4
F: Pcrglx protein
G: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,3816
Polymers201,3642
Non-polymers1,0174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-3 kcal/mol
Surface area58430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.616, 171.800, 342.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pcrglx protein


Mass: 100681.797 Da / Num. of mol.: 8 / Fragment: UNP residues 22-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS
#2: Polysaccharide
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 468.407 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2211m-1a_1-5][a21eEA-1a_1-5][a2112h-1b_1-5]/1-2-3/a2-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][b-L-4-deoxy-IdopA]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 306.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2211m-1a_1-5][a21eEA-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][b-L-4-deoxy-IdopA]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.3M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→171.17 Å / Num. obs: 255645 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 6.57 / Num. unique obs: 12654 / CC1/2: 0.974 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XQ3

5xq3


Resolution: 2.75→171.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.858 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26197 12900 5.1 %RANDOM
Rwork0.19583 ---
obs0.19921 242395 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.75→171.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56056 0 239 746 57041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01958102
X-RAY DIFFRACTIONr_bond_other_d0.0020.0251760
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.93579348
X-RAY DIFFRACTIONr_angle_other_deg1.0513118971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1657149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26723.9232832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85158431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99815324
X-RAY DIFFRACTIONr_chiral_restr0.0970.28412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02167198
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0214216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4613.69828578
X-RAY DIFFRACTIONr_mcbond_other2.463.69828577
X-RAY DIFFRACTIONr_mcangle_it3.8085.5435688
X-RAY DIFFRACTIONr_mcangle_other3.8085.54135689
X-RAY DIFFRACTIONr_scbond_it2.4323.79229524
X-RAY DIFFRACTIONr_scbond_other2.4323.79229525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8185.63143646
X-RAY DIFFRACTIONr_long_range_B_refined5.49341.84265667
X-RAY DIFFRACTIONr_long_range_B_other5.4941.84665622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 921 -
Rwork0.278 17830 -
obs--99.99 %

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